Mouse Colony Planner

Calculate timelines and cage numbers required for transgenic mouse breeding to optimize breeding costs.

Functions

• Timeline Calculation: Calculate time required for each stage based on breeding scheme
• Cage Planning: Estimate cage numbers needed for experiments
• Cost Estimation: Calculate total breeding costs (cage fees, husbandry fees, genotyping fees, etc.)

Usage

Command Line

python scripts/main.py --scheme <breeding_scheme> --females <number_of_females> --males <number_of_males> [options]

Parameters

Parameter	Description	Default
--scheme	Breeding scheme: heterozygote, homozygote, conditional	Required
--females	Starting number of females	Required
--males	Starting number of males	Required
--gestation	Gestation period (days)	21
--weaning	Weaning age (days)	21
--sexual-maturity	Sexual maturity age (days)	42
--cage-capacity	Maximum cage capacity	5
--cage-cost	Cage cost per day (CNY)	3.0
--genotyping-cost	Genotyping cost per mouse (CNY)	15.0
--target-pups	Target number of specific genotype mice	10

Breeding Scheme Descriptions

1. heterozygote (Heterozygote breeding): Heterozygote x Wild type → 50% Heterozygotes
2. homozygote (Homozygote breeding): Heterozygote x Heterozygote → 25% Homozygotes
3. conditional (Conditional knockout): Requires two-step breeding, introducing Cre/loxp system

Examples

# Heterozygote breeding scheme, starting with 10 females and 5 males, target to obtain 10 heterozygote offspring
python scripts/main.py --scheme heterozygote --females 10 --males 5 --target-pups 10

# Homozygote breeding, custom cycle parameters
python scripts/main.py --scheme homozygote --females 20 --males 10 --target-pups 20 --gestation 21 --weaning 21

# Conditional knockout scheme
python scripts/main.py --scheme conditional --females 15 --males 15 --target-pups 15

Output

• Timeline for each stage
• Cage numbers required at each stage
• Estimated total cost
• Breeding flowchart

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python/R scripts executed locally	Medium
Network Access	No external API calls	Low
File System Access	Read input files, write output files	Medium
Instruction Tampering	Standard prompt guidelines	Low
Data Exposure	Output files saved to workspace	Low

Security Checklist

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• Input file paths validated (no ../ traversal)
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no stack traces exposed)
• Dependencies audited

Prerequisites

# Python dependencies
pip install -r requirements.txt

Evaluation Criteria

Success Metrics

• Successfully executes main functionality
• Output meets quality standards
• Handles edge cases gracefully
• Performance is acceptable

Test Cases

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues: None
• Planned Improvements:
  • Performance optimization
  • Additional feature support